Structure of PDB 3dd2 Chain H

Receptor sequence

>3dd2H (length=258) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQFG

3D structure

• PDB: 3dd2 Crystal structure of an RNA aptamer bound to thrombin.
• Chain: H
• Resolution: 1.9 Å

Enzymatic activity

• Enzyme Commision number: 3.4.21.5: thrombin.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	H	H91 P92 R93 R101 R126 Q131 E164 R165 P166 D178 N179 R233 L234 K236 W237 K240	H87 P88 R89 R98 R123 Q131 E169 R170 P171 D183 N184 R245 L246 K248 W249 K252
BS02	0G6	H	H57 Y60A N98 L99 D189 A190 S195 S214 W215 G216	H43 Y47 N95 L96 D199 A200 S205 S226 W227 G228
BS03	MG	H	R221 K224	R233 K236

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity
• GO:0005509 calcium ion binding

Biological Process

• GO:0006508 proteolysis
• GO:0007596 blood coagulation

External links

• PDB: RCSB:3dd2, PDBe:3dd2, PDBj:3dd2
• PDBsum: 3dd2
• PubMed: 18971322
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)